Copter in-flight sudden thrust loss and altitude

I have an F-450 quadcopter with following specs:
Pixhawk 2.4.8 Flight Controller (Firmware v4.0.3)
30A ESCs
Emax MT-2216 810kV motor with 1045 props
Radiolink SE-100 GPS Module
3S, 50C, 5000mAh LiPo Battery
3S2P 18650 LG-HG2 (40A,600mAh) Battery

I have performed separate flights with both the LiPo and the Li-Ion batteries and experienced a sudden loss of thrust during flight (almost after 8 mins of flight with both the LiPo and Li Ion batteries). There is a “POTENTIAL THRUST LOSS” error on the HUD and the copter loses altitude suddenly. When I increase the throttle above 50%, it gains altitude but the same error happens after some interval of time. I’m tyring to figure out the reasons behind this sudden loss of thrust. Please help me understand if it is a,

  1. Firmware specific issue
  2. Wiring/ESC Calibration/Hardware Issue
  3. Battery issue

The link to the flight logs are,

With Li-Ion Battery

With Li-Po Battery

Thanks in advance!